>input_sequence_82402
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------------------------------------------------------ATGGGAAGGGCAATGGGGGCGGCGCT
CGTGCTGGCGGTCCTGGCCGTCGCGGCGGCCACGGCCGGGGCTGTTGACGGAGATGTCAAGTGCGCTGAGTGCGGCACGG
GCAC------GGTGCCGGTGCTGCCGCCGCCGCCGCCGTACTACTACTACAGCCCTCCACCTCCGGCGTCCTACTCCGGT
GTGTCCAACTGCCCGCCACCACCAGGGGGATACATCCAGATCGGCGGCTCGGGGCCGGGAAAAGGGCGCATGTACCCGCA
GGACCCCGGGTTCATGCCGTCCAGCGCGCCGCCCAGGCATGGGAGCAGCGCCGTCCACATCACGGTATGTTCGTTTGCGG
CGTTGGCGGTTCTACGGGCCTTTTGGTGA---------------------------------------------------
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>chr3A_1_TraesCS3A01G232200
GGTCGGGAGGACCTCCCGTGTGGCCCAAGCGGGGGGCAAGATCGAGTAAACGATTAAGAATCGGGCAACACCAAACTGGT
GCCCACATTTGACAGACCTCTCCCTTTTCCAACCCAACTACTATTAAGCTTTGCTTTCACCCGCAAAAAAAACAAAGTTT
GCTTCGCGATGAATATTCTACTGTAGCGCACTTGATGAGTAGCAAGCATGTGTAGAGTGAGTTTGAGCAGCCACATGCAA
AATGCATTAAAAATTCGTGCCAAGCA--------GGCCAGGCTCGATGCATGACATCCAGACCAGTCACATGGCAGCCGC
ACACACAAGGACAGATCGGAAGCTTCTTCTCGCTTTATCAAACTTGGTACGGGGGCGAAGCCAACTTTAAGCAAAGCTCC
CCGTAGTTGGGCTCCAACGAGGACTCCACGTTCCCCACACTCGCACGACGCTCGCAGCTAG------CTTGTTGCTTGAC
GCGTCGTCGTCCTCGCTGCGATCGCCTCGCAGCCGCACACGCACATGCACATGTTGACGACCACCGCGCGCGTCGGTGGC
ACCCCTCCAGCGAACGCACCCATCGCGCACCGCCGCGCCGAGCTCGCCCCCATAATGCACGCTCATGCATGTGGCCGACC
TGATCCGCGGACCCACGGATTTAGCGGCCGGCACATGGTCGTCGCTTTCGAGCCATACCGGAGGTTAGCCGCCAGCTCAG
GAGGTACCGCTGCTACCTTTCTCCTTGATGCACCAGCACAGTTACGCCTTCGCCTGCTTCTAAACCTACCGCCCCCATTC
TAACGAATCCCAAGCTCCCAACTAACATTCCTCCTCCATTCCACTCCTACTTTGTGGATCGTGACAGCATCATAAGAAGG
CTGGCCGGGAGGAGGGCCAGCACGGCCGCACCATAACCACCATAGCGCTTCTTACCGAGCCACACAACTTTCGCTCCTAT
AGCCTCGTAGCCAACGCCCGAACGCTCATCGTGGATAGGATGCGGCGGCCGGCCATGGGAAGGGCAATGGGGGCGGCGCT
CGTGCTGGCGGTCCTGGCCGTCGCGGCGGCCACGGCCGGGGCTGTTGACGGAGATGTCAAGTGCGCTGAGTGCGGCACGG
GCAC------GGTGCCGGTGCTGCCGCCGCCGCCGCCGTACTACTACTACAGCCCTCCACCTCCGGCGTCCTACTCCGGT
GTGTCCAACTGCCCGCCACCACCAGGGGGATACATCCAGATCGGCGGCTCGGGGCCGGGAAAAGGGCGCATGTACCCGCA
GGACCCCGGGTTCATGCCGTCCAGCGCGCCGCCCAGGCATGGGAGCAGCGCCGTCCACATCACGGTATGTTCGTTTGCGG
CGTTGGCGGTTCTACGGGCCTTTTGGTGATCGGTCTGCAGCAGTTGCGCGGCCATCGTCTCCGTTACGTGTCGCGACGGA
AGGACGGAGACGTGCCGGCGTTCCATGGATCTCCTGTGTATGCATTCACCTTGTAATAATTCTTACTGGTCATATGTTTT
GTAGTTCTTGCAATGCATCAAGCTTCTTCTTTTTTTGTTTCTCTCATTTTTGTTGTTACAGAACTTTTACTTGTAACAAA
TTAGTTGCAAATCAATGGAACTAGCAGGTCATGGTGGGTATGAGAATGTGTTATT-CGTGGGTGATCTTTTTGGCTTTTT
TTTCTTTCTTG-AAACAACTTTCTTCTTGTTCTTTGGGCAGAAAGGCTTCAGGCCTGGCTGTTTAAGTATTGGATTCCCG
GATCATAAAGTTTACAACTTGAAGAACCCCACCACAAGGGTAAGCGATTTCAAATGGTTTATCAACAACAACAACAATAA
TAACAAACAACAAATAGGTAAAATGGCTAAGCTATACAGCTGTTACTGACAATTTTGCTTCCGTTTTTGGAGAAGGGAAA
GTTCTGACATGATGCGATCATACCAGTTTGTTCAAAGACCAGCTCTAAGTAGCTTTTTG-GGATCAATTATAGCTTAGAA
ATTGGTGGATCTATGGGGAACC-C-AGTTCTTCTCACAAGGACTCTGTGCATGCAAAATGGGCCTAGCCAGTCGTGAT-A
TTTCATTACAATGCACATTCTTTCT-------------TTGCAACCGTTAATGACGCC----------------------
-------------------AACTAGACAATGATCATTGTCTAGTTTTTCCCCCCGCAAGAAAACTAGACAATGATCAAAT
GTGTGCCCCTTTTAGCTTTGCGTATAAGTTAAAAACTTCATCAACAAGCCTAACTATCATCAATTTAACTTCAGCAACAA
AAATGCCTAGGCTTGGAATGAAAGACCAGAGAATGTGGAGCCTTGCCAAATGCTCTTCCACAAGCTTATGTGAACTAGTC
AAAGGTTGCGGTCCTAGCGTAAAACGATCTTCTCTAACCACAAGGTGCA
>chr3D_134
CTTTACCCTG----------------------------------------------------------------------
--------------------------------------------------------------GAAAAAACTATTAAGCTA
GCTCCGCGAAGAATATTCT-----AGCGCACTTGATGAGTAGCAAGCATGTGTAGAGTGAGTTTCCACGGCAACATGCAA
AATGCATTAAAAATCCGTGCCAAGCAAGCAAGCAGGCCAGGATCAATGGATGAAT------CCAGTCACATGGCAGCCGC
ACACACGAGGACAGATCGGAAGCTTCTTCCCGCTTTATCAAACTTGGTACGGGGGCGAAGCCAACTTTAAGCCAAGCTCC
CCGTAGTTGGGCTCCAACGACGACTCCACGTTCCCCACACTCGCACGACGCTAGCAGCTAGTACTAGCTTGTTGCTTGAC
GCGTCGTCGTCCTCGCTGCGATCGCCTCGCAGC------CGCACATGCACATGTTGACGACCACCGCGCGCGTCGGTGGC
ACCCCTCCAGCGAACGCATCCATCGCGCACCGCCGCGCCGAGCTCGCTCCCATAATGCACGCTCATGCATGTGGCCGACC
TGATCCGCGGACCCACGGATTTAGCGGCCGGCACATGGTCGTCGCTTTCGAGCCATACCGGAGGTTAGCCGCCAGCTCAG
GAGGTACCAATGCTGCCTGCCTCCTTGATGCAGCAGTACAGTTACGCCTTCCTCTGCTTCCAAACCTACTGCCCCCGTTC
TAACGAATCCCAACTAAT--------ATTCCTCCTCCATTCTACTCCTACTTTGTGGATCGTGACAGCATCATAAGAAGG
CTGGCGGGGAGGAGGGCCAGCACGGCCACACCATAACCACCATAGCGCTTCTTACCGAGCCACACTACTTTCGCTCGTAT
AGCCTCGTAGCCAACGCCCGAACGCTCACCGTGGATAGGATGCGGCGACCGGCCATGGGAAGGGCAATGGCGCCGCTCCT
CGTGCTGGCGGTCCTGGCCGTCGCGGCGGCCACGGCCGGGGCTGTTGACGGAGATGTCAAGTGCGCTGAGTGCGGCACGG
GCACGGTGCCGGTGCCCGTGCTGCCGCCGCCGCCGCCGTACTACTACTACAGCCCTCCGCCTCCGGCGTCCTACCCCGGT
GTGTCCAACTGCCCGCCGCCGCCAGGGGGGTACATCCAGATCGGGGGCTCGGCGCCGGGCAAAGGGCGCATGTACCCGCA
GGACCCCGGGTTCATGCCATCCAGCGCGCAGCCCAGGCATGGGAGCCGCGCCGTCCACTTCACGGTATGTTCGTTTGCGG
CGTTGGCGATTCTACGGGCCTTTTGGTGATCGATCTGCGGCAACTGCGCGGCCATCGTCTCCGTTACGTGTCGCGACGGA
AGGACAGAGACGTGCCGGCGTTCCATGGATCTCCTGTGTATGCATTCACCTTGTAATAATTCTTACTGGTCATATGTTTT
GTAGTTCTTGTAATACATCAAGCT-------CCTTTTTCTCAATTTTGTTTCTTGTTACAGAACTTTTACTTGTAACAAA
TTAGTTGCAAATCAATGGAACTAGCAGGTCATGGTGGGTATGAGAATGTGTTATT-CGTGGGTGATCTTTTTGGCTTTTC
TTTCTTTCTTG-AAACAACTTTCTTCTTGTTCTTTGG-CAGAAAGGCTTCAGGCCTGGCTGTTTAAGTATTGGATTCCCA
GATCATAAAGTTTACAACTCGAAGAACCCCGCCGCAAGGGTAAGCGACTTCAAATGGTTTATCAACAACAACAA------
------ACAACAAATGGGCAAAATGGCTAAGCTATACGACTCTTACTCACAATTCTGCTTCCGTTTCCGGAGAAGGGAAA
GTTGTGACATGATGCGATCATGCCAGTTTGTTCGAAGACCAGCTCTAAGTAGCTTTTTCCGGATCAACTATGGCTTAGAA
ATTGGTGGATCTATGGGGAA-CGC-AGTTCTTCTCACAAGGATTCCGTGCATGCAAAATGGGCCTAGCAAGTCGTGATAA
TTTCATCACAATGCACATTCTTTCTCACTCCTCTTTCTTTGCAGCCGTTAATGACGCG----------------------
-------------------AACTAGACAATGATCA------------------------------------------AAT
GCGTGCCCCTTTTTGCTTTGCGTACAAGTTAAAATTTTCAGCAACAAGGCTAACTATCATCAGTTTAACTTCAGCAACAA
AAATGCCTAGGCTTGGAATGAAAGATCAGACCATGTGGAGCCTTGCCAAATCCTCTTCCACAAGCTTCTGCGAACTAGTC
AAAGGCTGCGGTCCTAGCGTAAAACGATCTTCTCTGACCACAGGGTGCA
>chr3B_243
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--TGCATTAAAAATCCGTGC----CAAGCAAGCAGGCCAGGATCAATGGATGACATCAAGACCAGTCACATGGCAGCCGC
ACACACAAGGACAGATCGGAAGCTTCTTCCCGCTTTATCAAACTTGGTACGGGGGCGAAGCCAACTTTAAGCAAAGCTCC
CCGTAGTTGGGCTCCAACGAGGAGTCCACGTTCTCCACACTCGCACGACGCGAGCAG------CTAGCTTGTTGCTTGAC
GCGTCGTCGTCCTCGC--------------AGC------CGCACATGCACATGTTGACGACCACCGCGCGCGTCGGTGGC
ACTCCTCCAGCGAACGCATCCATCGCGCACCGCCGCGCCGAACTCGCTCCCATAATGCACGCTCATGCATGTGGCCGACC
TGATCCGCGGACCCACGGATTTAGCGGCCGGCACATGGTCGTCGCTTTCGAGCCATACCGGAGGTTAGCAGCCAGCTCAG
GAGGTACCGATGCTACCTGCCTCCTTGATGCAGCAGTACAGTTACGCCTTCCTCTGCTTCTAAACCTACTGCCCCCGTTC
TAACGAATCCCAACTAAT--------ATTCCTCCTCCATTCTACTCCTACTTTGTGGATCGTGACAGCATCATAAGAAGG
CTGGCCGGGAGGAGGGCCAGCACGGCCACACCATAACCACCATAGCGGTTCTTACCGAGCCACACAACTTTCTCTCGTAT
AGGCTCGTAGCCAACGCCCGAACGCTCACCGTGTATAGGATGCGGCGGCCGGCCATGGGAAGAGCAATGGCGCCGCTCCT
CGTGCTGGCGGTCCTCGCCGTCGCGGCGGCCAGGGCCGGGGCTCTTGACGGAGATGTCAAGTGCGCTGAGTGCGGCACGG
GCAC------GGTGCCCGTGCTGCCGCCGCCGCCGCCGTACTACTACTACAGCCCTCCACCTCCGGCGTCCTACCCCGGT
GTCTCCAACTGCCCGCCGCCGCCAGGGGGGTACATCCAGATCGGGGGCTCGGCGCCGGGCAAAGGGCGCATGTACCCGCA
GGACCCCGGGTTCATGCCATCCAGCGCGCCGCCCAGGCATGGGAGCAGCGCCGTCCATTTCACCGTATGTTCGTTTGCGG
CGTTGGCGATTCTACGGGCCTTTTGGTGATCGATCTGCAGCAATTGCGCGGCCACCGTCTCCGTTACGTGTCGCGACGGA
AGGACAGAGACGTGCCGGCGTTCCATGGATCTCCTGTGTATGCATTCACCTTGTAATAATTCTTACTGGTCATATGTTTT
GTAGTTCTTGCAATGCATCAAGCT-------TTTTTTTTCCTCTTAATTTTGTTGTTACAGAACTTTTACTTGTAACAAA
TTAGTTGCAAATCAATGGAACTAGCAGGTAATGGTGGGTATGAGAATGTGTTATT-CGTGGGTGATCTTTTTGGCTTTT-
TTTCTTTCTTGAAAACACCTTTCTTCTCGTTCTTTGGGCAGAAAGGCTTCAGGCCTGGCTGTTTAACTATTGGATTCCCA
GATCATAAAGTTTACAACTCAAAGAACCCCGCCGCAAGGGTAAGCGATTGTAAATGGTTTATCAACAACAACAA------
------ACAACAAATGGGTAAAATGGCTAAGCTATACGACTGTTACTGACAATTCTGCTTCCGTTTCTGGAGAAGGAAAA
GTT--GACATGATGTGATCATGCCAGTTTGTTCAAAGACCAGCTCTAAGTAGCTTTTTC-GGATCAACTATAGCTTAGAA
ATTGGTGGATCTATGGGGAA-C-C-AGTTCTTCTCACAAGGACTTTGTGCATGCAAAATGGACATAGCACGTCGTGATAA
TTTCATCACAATGCACATTCTTTCTCACTCCTCTTTCATTGCAACTGTTAATGACACC----------------------
-------------------AACTAGACAATGATCA------------------------------------------AAT
GCGTGCCCCTTTT-GCTTTGCGTATAAGTTAAAAACTTCAGCAACAAGCCTAACTATCATCAATTTAACTTCAGCAACAA
AAATGCCTAGGCTTGGAATGAAAGATCAGACAATGTGGAGCCTTGCCAAATCCTCTTCCACAAGCTTATGCGAACTAGTC
AAAGGTTGCGGTCCTAGCGTAAAACGATCTTCTCTAACCACAAGGTGCA
>chr3A_1573
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------------------------------------------------------------------------GTAACAAA
TTAGTTGCAAATCAATGGAACTAGCAGTTCATGGTGGGTATGAGAATGTGTTTATCCGTGGGTGATCTTTTTGGCTTT-C
TTTCTTTCTTG-AAACACCTTTCTTCTTGTTCTTTGGGCAGAAAGGCTTCAGGCCTGGCTGTGTACGTATTGGATTCCTA
GATCATAAAGTTCACAACTCTAAGAACCCCGCCGCAAGGGTAAGCGATTTCAAATGGTTTATCAATAACAACAACAACAA
CAAC-----------GGGTAAAATGGCTAAGCTATATGACTGTTACTGACAATTATGCTTCTGTTTTTGGAGAAGGGAAA
GTTCTGACATGACGCGATCATACCCGTTTGTTCAAAGACCAGCTCTAAGTAGCTTTTTG-GAATCAACTATAGCTTAGAA
ATTGGTGGATATATGGGGAA-C-CCAGTTCTTCTCACAAGGACTCTGTGCATGCAAAATGGGCCTAGCGAGTCGTGAT-A
TTTCATTACAATGCACATTCTTTCT-------------TTGCAACCGTTAACGACGCCAACTAGACAATGATCATTGTCT
AGTTTTTCCCCCCGCAAAAAACTAGACAATGATCA------------------------------------------AAT
GTGTGCCCCTTTTTGCTTTGCGTATAAGTTAAAAACTTCAGCAACAAGCCTAACTATCATCAATTTAACTTCAGCAACAA
AAATGCCTAGGCTTGGAATGAAAGACCTGACAATGTGGAGCCTTGCCAAATGATCTTCCATAAGCTTATGCGAACTAGTC
AAAGGTTGCAGTCCTAGCGTAAAAATATCTTCTCTAACCACAAGGTGCA
>SNPs
SS-SSSSSS-SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS-S-----SS-SS---S-S
---S-----S---------SSSSS----------------------------------------SSS-S--S--------
--------------S--------------------------S--S---S--------S----------------------
-----------------------------S--------------------------------------------------
----------------------------------------------------S---------------------------
---------------------------------SSSSSS-----------------------------------------
------------------S----------------------------S--------------------------------
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---------S--------SS------------S---S--------------SS----------------S------S---
-------------SSSSSSSSSSSSS---------------S--------------------------------------
---------------------------S------------------------------------------------S---
----------------------------S-----------------------------------------S-S--SSS--
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----------------S---------------------------------------------------------S-----
-----------------S--S--------S--------------S-------S------S--------------------
------------------S---------------------------------------S---------------------
--------S-----------------------S---------S-------------------------------------
-----S--------------------------------------------------------------------------
------------------------SSSSSSS-----S-------S-----------------------------------
-------------------------------------------------------------------------------S
-------------------------------------------------------------------------------S
-------------------S----------S--S-------------------------------------------S--
S---SS---------S---------------------SS---------------S-------------------------
-------------------------------------------------------------------S------------
--------------------S-----------------------------------------------S-----------
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-----------------------------------SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS---
-------------S--------------------------S---------------------------------------
------------------------------S---------------------------------------S---------
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>forward_823
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---CGAATCCCAAGCTCCCAACT---------------------------------------------------------
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>reverse_1780
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-------------------TGAAGAACCCCACCACAAGG-----------------------------------------
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